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Started by upstream project "BIOFORMATS-test-repo" build number 47 originally caused by: Started by upstream project "Trigger" build number 54 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins9803631238061748761.sh + '[' samples = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_6727_merge_ci -v /uod/idr/repos/curated/samples:/data -v /uod/idr-scratch/merge-ci/curated/samples:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 Buildfile: /bio-formats-build/bioformats/components/test-suite/build.xml [echo] isSnapshot = true init-title: [echo] ----------=========== bio-formats-testing-framework ===========---------- init-timestamp: init: copy-resources: compile: [resolver:resolve] Resolving artifacts compile-tests: [resolver:resolve] Resolving artifacts [javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] 1 warning test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 01:24:09,618 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:24:09,620 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:24:09,620 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:24:09,621 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:24:09,622 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:24:09,622 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:24:09,623 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:24:09,623 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:24:09,623 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:24:09,624 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:24:09,625 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:24:09,625 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:24:09,825 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:24:09,825 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:24:09,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:24:09,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:24:09,856 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:24:09,856 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:24:09,857 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:24:09,857 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:24:09,857 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:24:09,858 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:24:09,858 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 235 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-28 01:24:09,867] [main] java.version = 17.0.2 [testng] 01:24:09,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:24:09,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:09,915 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-28_01-24-09.log] [testng] 01:24:09,917 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-04-28 01:24:09,919] [main] testng.directory = /data [testng] [2024-04-28 01:24:09,919] [main] testng.configDirectory = /config [testng] [2024-04-28 01:24:09,929] [main] testng.multiplier = 1.0 [testng] [2024-04-28 01:24:09,929] [main] testng.in-memory = false [testng] [2024-04-28 01:24:09,930] [main] testng.allow-missing = false [testng] [2024-04-28 01:24:09,930] [main] user.language = en [testng] [2024-04-28 01:24:09,930] [main] user.country = ${user.country} [testng] [2024-04-28 01:24:09,930] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-28 01:24:29,765] [main] ---------------------------------------- [testng] [2024-04-28 01:24:29,765] [main] Total files: 164 [testng] [2024-04-28 01:24:29,766] [main] Scan time: 19.835 s (120 ms/file) [testng] [2024-04-28 01:24:29,766] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-28 01:24:38,803] [pool-1-thread-1] Initializing /data/ome/Adultmidsection.lsm: [testng] 01:24:38,803 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:24:38,803 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:38,805 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-28_01-24-38.log] [testng] 01:24:38,805 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bb9bd9a - End of configuration. [testng] [2024-04-28 01:24:38,837] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 01:24:38,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:24:38,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:38,839 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-28_01-24-38.log] [testng] 01:24:38,839 |-INFO in ch.qos.logback.core.sift.SiftProcessor@af8b938 - End of configuration. [testng] [2024-04-28 01:24:38,880] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 01:24:38,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:24:38,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:38,881 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-28_01-24-38.log] [testng] 01:24:38,881 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20634cc8 - End of configuration. [testng] [2024-04-28 01:24:38,892] [pool-1-thread-10] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:24:38,892 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:24:38,892 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:38,893 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-28_01-24-38.log] [testng] 01:24:38,894 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63cd54bd - End of configuration. [testng] [2024-04-28 01:24:38,938] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 01:24:38,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:24:38,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:38,939 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-28_01-24-38.log] [testng] 01:24:38,939 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ddcfad7 - End of configuration. [testng] [2024-04-28 01:24:38,949] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:24:38,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:24:38,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:38,950 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-28_01-24-38.log] [testng] 01:24:38,950 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5cbfaf13 - End of configuration. [testng] [2024-04-28 01:24:38,963] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 01:24:38,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:24:38,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:38,964 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-28_01-24-38.log] [testng] 01:24:38,965 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bee7c5e - End of configuration. [testng] [2024-04-28 01:24:39,007] [pool-1-thread-6] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 01:24:39,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:24:39,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:39,009 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-28_01-24-39.log] [testng] 01:24:39,009 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fd6dd35 - End of configuration. [testng] [2024-04-28 01:24:39,145] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 01:24:39,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:24:39,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:39,147 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-28_01-24-39.log] [testng] 01:24:39,147 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50380ee1 - End of configuration. [testng] [2024-04-28 01:24:39,160] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff: [testng] 01:24:39,160 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:24:39,160 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:39,161 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-28_01-24-39.log] [testng] 01:24:39,162 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5783815f - End of configuration. [testng] [2024-04-28 01:24:39,229] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 01:24:39,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:24:39,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:39,230 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-28_01-24-39.log] [testng] 01:24:39,231 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7038b55 - End of configuration. [testng] [2024-04-28 01:24:39,254] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 01:24:39,254 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:24:39,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:39,255 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-28_01-24-39.log] [testng] 01:24:39,256 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5cf677b2 - End of configuration. [testng] [2024-04-28 01:24:40,625] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-04-28 01:24:40,999] [pool-1-thread-2] Initializing /data/sdub/sdub.pattern: [testng] [2024-04-28 01:24:41,201] [pool-1-thread-10] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-04-28 01:24:41,457] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-04-28 01:24:41,528] [pool-1-thread-4] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-04-28 01:24:41,559] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-04-28 01:24:41,857] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-04-28 01:24:41,867] [pool-1-thread-12] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-04-28 01:24:42,090] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-04-28 01:24:42,097] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-04-28 01:24:42,105] [pool-1-thread-11] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-04-28 01:24:42,112] [pool-1-thread-4] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-04-28 01:24:42,284] [pool-1-thread-5] Initializing /data/ome/worm.tiff: [testng] [2024-04-28 01:24:42,395] [pool-1-thread-7] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-04-28 01:24:42,526] [pool-1-thread-3] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-04-28 01:24:42,835] [pool-1-thread-3] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-04-28 01:24:43,007] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-04-28 01:24:43,300] [pool-1-thread-6] Initializing /data/ome/654Atemp.stk: [testng] [2024-04-28 01:24:43,401] [pool-1-thread-4] Initializing /data/ome/embryo.lsm: [testng] [2024-04-28 01:24:43,583] [pool-1-thread-2] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-04-28 01:24:43,855] [pool-1-thread-7] Initializing /data/ome/C1.lsm: [testng] [2024-04-28 01:24:43,987] [pool-1-thread-1] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-04-28 01:24:44,922] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] [2024-04-28 01:24:44,995] [pool-1-thread-3] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-04-28 01:24:45,050] [pool-1-thread-10] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-04-28 01:24:46,040] [pool-1-thread-12] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-04-28 01:24:46,064] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-04-28 01:24:46,423] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-04-28 01:24:46,654] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-04-28 01:24:46,665] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-04-28 01:24:46,783] [pool-1-thread-12] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-04-28 01:24:46,846] [pool-1-thread-2] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-04-28 01:24:46,993] [pool-1-thread-5] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-04-28 01:24:47,289] [pool-1-thread-4] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-04-28 01:24:47,346] [pool-1-thread-6] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-04-28 01:24:47,356] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-04-28 01:24:47,407] [pool-1-thread-3] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-04-28 01:24:47,616] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-04-28 01:24:47,700] [pool-1-thread-5] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-04-28 01:24:47,792] [pool-1-thread-3] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-04-28 01:24:47,893] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-04-28 01:24:47,941] [pool-1-thread-4] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-04-28 01:24:48,001] [pool-1-thread-12] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-04-28 01:24:48,171] [pool-1-thread-3] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-04-28 01:24:48,246] [pool-1-thread-11] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-04-28 01:24:48,469] [pool-1-thread-12] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-04-28 01:24:48,582] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 2 minutes 17 seconds Finished: SUCCESS